5LVU

XiaF (apo) from Streptomyces sp.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JBR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	1.6 M ammonium sulfate, 0.1 M HEPES, 0.1 M sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
4.48	72.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.54	α = 90
b = 166.54	β = 90
c = 98.97	γ = 120

Symmetry
Space Group	P 62 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2015-12-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.6	30	99.6	0.085	16.5	10.9		25318

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.7	99.7		0.563	4.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2JBR	2.6	15	24035	1265	99.65	0.18398	0.18223	0.21759	RANDOM	64.744

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.9	0.9		0.9		-2.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.319
r_sphericity_free	23.471
r_dihedral_angle_4_deg	17.51
r_dihedral_angle_3_deg	15.468
r_sphericity_bonded	11.443
r_dihedral_angle_1_deg	4.131
r_long_range_B_refined	3.554
r_long_range_B_other	3.381
r_mcangle_it	3
r_mcangle_other	3
r_scangle_other	2.744
r_mcbond_it	2.27
r_scbond_it	2.264
r_scbond_other	2.256
r_mcbond_other	2.233
r_angle_refined_deg	0.788
r_angle_other_deg	0.689
r_rigid_bond_restr	0.554
r_chiral_restr	0.04
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2954
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing